From 2b49ea5130e34e035ab35ab7b0f52686ef88cf86 Mon Sep 17 00:00:00 2001 From: Sam Isaacson Date: Mon, 22 Jul 2024 11:38:29 -0400 Subject: [PATCH 1/2] remove bondgraphs from docs and fix SBMLImporter link --- docs/src/index.md | 3 +-- 1 file changed, 1 insertion(+), 2 deletions(-) diff --git a/docs/src/index.md b/docs/src/index.md index 88c1ae2a41..5781e5b5d0 100644 --- a/docs/src/index.md +++ b/docs/src/index.md @@ -47,11 +47,10 @@ etc). - [SciMLSensitivity.jl](https://github.com/SciML/SciMLSensitivity.jl) can be used to compute local sensitivities of functions containing forward model simulations. #### [Features of packages built upon Catalyst](@id doc_index_features_other_packages) -- Catalyst [`ReactionSystem`](@ref)s can be [imported from SBML files](@ref model_file_import_export_sbml) via [SBMLImporter.jl](https://github.com/SciML/SBMLImporter.jl) and [SBMLToolkit.jl](https://github.com/SciML/SBMLToolkit.jl), and [from BioNetGen .net files](@ref model_file_import_export_sbml_rni_net) and various stoichiometric matrix network representations using [ReactionNetworkImporters.jl](https://github.com/SciML/ReactionNetworkImporters.jl). +- Catalyst [`ReactionSystem`](@ref)s can be [imported from SBML files](@ref model_file_import_export_sbml) via [SBMLImporter.jl](https://github.com/sebapersson/SBMLImporter.jl) and [SBMLToolkit.jl](https://github.com/SciML/SBMLToolkit.jl), and [from BioNetGen .net files](@ref model_file_import_export_sbml_rni_net) and various stoichiometric matrix network representations using [ReactionNetworkImporters.jl](https://github.com/SciML/ReactionNetworkImporters.jl). - [MomentClosure.jl](https://github.com/augustinas1/MomentClosure.jl) allows generation of symbolic ModelingToolkit `ODESystem`s that represent moment closure approximations to moments of the Chemical Master Equation, from reaction networks defined in Catalyst. - [FiniteStateProjection.jl](https://github.com/kaandocal/FiniteStateProjection.jl) allows the construction and numerical solution of Chemical Master Equation models from reaction networks defined in Catalyst. - [DelaySSAToolkit.jl](https://github.com/palmtree2013/DelaySSAToolkit.jl) can augment Catalyst reaction network models with delays, and can simulate the resulting stochastic chemical kinetics with delays models. -- [BondGraphs.jl](https://github.com/jedforrest/BondGraphs.jl), a package for constructing and analyzing bond graphs models, which can take Catalyst models as input. ## [How to read this documentation](@id doc_index_documentation) The Catalyst documentation is separated into sections describing Catalyst's various features. Where appropriate, some sections will also give advice on best practices for various modeling workflows, and provide links with further reading. Each section also contains a set of relevant example workflows. Finally, the [API](@ref api) section contains a list of all functions exported by Catalyst (as well as descriptions of them and their inputs and outputs). From f6fc814318c63e6549aaf8fdc6754b3dea3cf5f8 Mon Sep 17 00:00:00 2001 From: Sam Isaacson Date: Mon, 22 Jul 2024 11:44:52 -0400 Subject: [PATCH 2/2] remove extraneous note --- .../model_simulation/examples/periodic_events_simulation.md | 3 --- 1 file changed, 3 deletions(-) diff --git a/docs/src/model_simulation/examples/periodic_events_simulation.md b/docs/src/model_simulation/examples/periodic_events_simulation.md index ab171a68d3..b9bbfd9e76 100644 --- a/docs/src/model_simulation/examples/periodic_events_simulation.md +++ b/docs/src/model_simulation/examples/periodic_events_simulation.md @@ -78,6 +78,3 @@ If we directly plot $l$'s value, it will be too small (compared to $X$ and $Xᴾ @unpack X, Xᴾ, l = circadian_model plot(sol; idxs = [X, Xᴾ, 150*l], labels = ["X" "Xᴾ" "Light amplitude"]) ``` - -!!! note - If you wish to reproduce this in a jump simulation, remember to make appropriate modifications (like using `setu` instead of `setp`). \ No newline at end of file